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DEVELOPMENT OF EPIC GENETIC MARKERS AND THE UTILITY OF A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL APPROACH TO EXAMINING PATTERNS OF GENETIC DIVERSITY
Citation:
Sloss, B. L. AND M J. Bagley. DEVELOPMENT OF EPIC GENETIC MARKERS AND THE UTILITY OF A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL APPROACH TO EXAMINING PATTERNS OF GENETIC DIVERSITY. Presented at Society of Environmental Toxicology and Chemistry, Baltimore, MD, November 11-15, 2001.
Impact/Purpose:
The objective of this task is to develop molecular indicators to evaluate the integrity and sustainability of aquatic fish, invertebrate, and plant communities (GPRA goal 4.5.2). Specifically, this subtask aims to evaluate methods for the measurement of:
fish and invertebrate community composition, especially for morphologically indistinct (cryptic) species
population genetic structure of aquatic indicator species and its relationship to landscape determinants of population structure (to aid in defining natural assessment units and to allow correlation of population substructure with regional stressor coverages)
genetic diversity within populations of aquatic indicator species, as an indicator of vulnerability to further exposure and as an indicator of cumulative exposure
patterns of temporal change in genetic diversity of aquatic indicator species, as a monitoring tool for establishing long-term population trends.
Description:
Use of population genetic measures for assessing the structure of natural populations and the condition of biological resources has increased steadily since the 1970's. Traditionally, genetic diversity within and among geographic areas is assessed based on a one-time sampling of select sites and measures of allelic frequencies. In addition to measuring spatial patterns of genetic diversity, population genetic measures of biological resources should include temporal data which indicate whether the observed patterns are the result of historical or contemporary processes. Allele frequency data from one-time sampling of populations are poor indicators of temporal processes. The use of individual gene genealogies combined with allele frequency data permit the inference of temporal processes from one-time samples of spatial patterns. The value of this phylogeographic approach has been clearly demonstrated with mitochondrial DNA data; however, reliance on a single locus for any genetic study is error-prone. We are developing 12-16 EPIC (Exon-Primed, Intron-Crossing) primers designed to amplify homologous intron regions within teleost genomes. This development will aid in fish population analyses, including stock identification, estimates of gene flow, effective population size, and effects of environmental change. In addition, multi-species assessment of homologous markers permits a more accurate assessment of patterns of biodiversity and the condition of biological resources across a wide geographical area. Intron regions from eight nuclear genes (c-myc proto-oncogene, K-ras, Pax transcription factor, 40S ribosomal protein 24, GTPase, ependymin, and alpha crystallin) have been amplified and cloned for creek chub (Semotilus atromaculatus), central stoneroller (Campostoma anomalum), white sucker (Catostomus commersoni), brown bullhead (Ameiurus nebulosus) and/or green sunfish (Lepomis cyanellus). These loci will be combined with mtDNA data to analyze the distribution of genetic diversity of creek chub, central stoneroller and white sucker within USEPA's Mid-Atlantic Integrated Assessment (MAIA) study area.